TRIM39-RPP21 (TRIM39-RPP21 readthrough) - Rat Genome Database

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Gene: TRIM39-RPP21 (TRIM39-RPP21 readthrough) Homo sapiens
Analyze
No known orthologs.
Symbol: TRIM39-RPP21
Name: TRIM39-RPP21 readthrough
RGD ID: 5013861
HGNC Page HGNC:38845
Description: Predicted to enable ubiquitin protein ligase activity and zinc ion binding activity. Predicted to be involved in several processes, including negative regulation of proteasomal ubiquitin-dependent protein catabolic process; positive regulation of apoptotic signaling pathway; and protein stabilization. Located in cytosol.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: Rpp21 domain-containing TRIM protein; TRIM39-RPP21 read-through transcript; TRIM39R
RGD Orthologs
Alliance Genes
More Info homologs ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38630,329,311 - 30,346,858 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl630,328,907 - 30,346,854 (+)EnsemblGRCh38hg38GRCh38
GRCh37630,297,088 - 30,314,635 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map6p22.1NCBI
HuRef630,095,213 - 30,112,765 (+)NCBIHuRef
CHM1_1630,299,166 - 30,316,719 (+)NCBICHM1_1
T2T-CHM13v2.0630,193,517 - 30,211,069 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
genetic disease  (IAGP)
megacolon  (IAGP)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cytoplasm  (IEA)
cytosol  (IDA)

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View

Human Phenotype
References

References - curated
# Reference Title Reference Citation
1. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:17601797   PMID:20967262   PMID:23707810   PMID:35271311  


Genomics

Variants

.
Variants in TRIM39-RPP21
13 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 6p22.3-21.33(chr6:18120520-30767516)x1 copy number loss Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052180]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052180]|See cases [RCV000052180] Chr6:18120520..30767516 [GRCh38]
Chr6:18120751..30735293 [GRCh37]
Chr6:18228730..30843272 [NCBI36]
Chr6:6p22.3-21.33		 pathogenic
NM_021253.3(TRIM39):c.1226T>C (p.Val409Ala) single nucleotide variant Malignant melanoma [RCV000067267] Chr6:30341928 [GRCh38]
Chr6:30309705 [GRCh37]
Chr6:30417684 [NCBI36]
Chr6:6p22.1		 not provided
NM_001199119.1(TRIM39-RPP21):c.1288+128C>T single nucleotide variant Lung cancer [RCV000096816] Chr6:30345701 [GRCh38]
Chr6:30313478 [GRCh37]
Chr6:6p22.1		 uncertain significance
GRCh38/hg38 6p25.2-21.33(chr6:3224310-30657190)x3 copy number gain See cases [RCV000138956] Chr6:3224310..30657190 [GRCh38]
Chr6:3224544..30624967 [GRCh37]
Chr6:3169543..30732946 [NCBI36]
Chr6:6p25.2-21.33		 pathogenic
GRCh38/hg38 6p25.3-12.3(chr6:156974-46789291)x3 copy number gain See cases [RCV000143497] Chr6:156974..46789291 [GRCh38]
Chr6:156974..46757028 [GRCh37]
Chr6:101974..46864987 [NCBI36]
Chr6:6p25.3-12.3		 pathogenic
GRCh37/hg19 6p25.3-q27(chr6:156975-170919482)x3 copy number gain See cases [RCV000512067] Chr6:156975..170919482 [GRCh37]
Chr6:6p25.3-q27		 pathogenic
GRCh37/hg19 6p25.3-q27(chr6:156975-170919482) copy number gain See cases [RCV000510595] Chr6:156975..170919482 [GRCh37]
Chr6:6p25.3-q27		 pathogenic
GRCh37/hg19 6p25.3-q27(chr6:108666-170980171)x3 copy number gain not provided [RCV000745403] Chr6:108666..170980171 [GRCh37]
Chr6:6p25.3-q27		 pathogenic
GRCh37/hg19 6p25.3-q27(chr6:60107-171054786)x3 copy number gain not provided [RCV000745400] Chr6:60107..171054786 [GRCh37]
Chr6:6p25.3-q27		 pathogenic
GRCh37/hg19 6p25.3-q27(chr6:165632-170919470)x3 copy number gain not provided [RCV000745404] Chr6:165632..170919470 [GRCh37]
Chr6:6p25.3-q27		 pathogenic
GRCh37/hg19 6p22.1-21.32(chr6:28130359-32108367)x3 copy number gain not provided [RCV000745592] Chr6:28130359..32108367 [GRCh37]
Chr6:6p22.1-21.32		 uncertain significance
GRCh37/hg19 6p22.1-q14.1(chr6:29455465-81447367) copy number gain not provided [RCV000767714] Chr6:29455465..81447367 [GRCh37]
Chr6:6p22.1-q14.1		 pathogenic
NC_000006.11:g.28005012_31683185del deletion Megacolon [RCV001290055] Chr6:28005012..31683185 [GRCh37]
Chr6:6p22.1-21.33		 likely pathogenic
NM_001369521.2(TRIM39):c.1340G>A (p.Arg447His) single nucleotide variant Inborn genetic diseases [RCV002919773] Chr6:30342132 [GRCh38]
Chr6:30309909 [GRCh37]
Chr6:6p22.1		 uncertain significance
NM_001369521.2(TRIM39):c.1441A>G (p.Ile481Val) single nucleotide variant Inborn genetic diseases [RCV002831335] Chr6:30342233 [GRCh38]
Chr6:30310010 [GRCh37]
Chr6:6p22.1		 uncertain significance
NM_001369521.2(TRIM39):c.804-187C>T single nucleotide variant Inborn genetic diseases [RCV002959822] Chr6:30340318 [GRCh38]
Chr6:30308095 [GRCh37]
Chr6:6p22.1		 uncertain significance
NM_001369521.2(TRIM39):c.804-226C>T single nucleotide variant Inborn genetic diseases [RCV002854941] Chr6:30340279 [GRCh38]
Chr6:30308056 [GRCh37]
Chr6:6p22.1		 likely benign
NM_001369521.2(TRIM39):c.1150G>A (p.Val384Met) single nucleotide variant Inborn genetic diseases [RCV003281460] Chr6:30341942 [GRCh38]
Chr6:30309719 [GRCh37]
Chr6:6p22.1		 uncertain significance
NM_024839.4(RPP21):c.159-10C>T single nucleotide variant Inborn genetic diseases [RCV003196477] Chr6:30345481 [GRCh38]
Chr6:30313258 [GRCh37]
Chr6:6p22.1		 uncertain significance
NM_001369521.2(TRIM39):c.804-232A>C single nucleotide variant Inborn genetic diseases [RCV003342200] Chr6:30340273 [GRCh38]
Chr6:30308050 [GRCh37]
Chr6:6p22.1		 likely benign
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:161
Count of miRNA genes:111
Interacting mature miRNAs:112
Transcripts:ENST00000513556
Prediction methods:Microtar, Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.

Markers in Region
RH94264  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37630,313,299 - 30,314,304UniSTSGRCh37
Celera631,911,494 - 31,912,499UniSTS
Cytogenetic Map6p22.1UniSTS
HuRef630,111,429 - 30,112,434UniSTS
GeneMap99-GB4 RH Map6118.72UniSTS


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system sensory system entire extraembryonic component
High
Medium
Low 1 3 6 1 1 17 1
Below cutoff 74 1 84 51 226 55 188 34 78 107 145 192 5 3

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000623385   ⟹   ENSP00000485378
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl630,328,907 - 30,346,854 (+)Ensembl
RefSeq Acc Id: NM_001199119   ⟹   NP_001186048
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38630,329,311 - 30,346,858 (+)NCBI
GRCh37630,297,088 - 30,314,635 (+)ENTREZGENE
HuRef630,095,213 - 30,112,765 (+)ENTREZGENE
CHM1_1630,299,166 - 30,316,719 (+)NCBI
T2T-CHM13v2.0630,193,517 - 30,211,069 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001186048 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein ABR92635 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSP00000446632.2
  ENSP00000446993.2
  ENSP00000485378
  ENSP00000485378.1
Reference Protein Sequences
RefSeq Acc Id: NP_001186048   ⟸   NM_001199119
- UniProtKB: A0A096LP39 (UniProtKB/TrEMBL),   A0A0G2JKY0 (UniProtKB/TrEMBL),   A0A140TA46 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSP00000485378   ⟸   ENST00000623385
Protein Domains
B box-type   B30.2/SPRY   RING-type


Additional Information

Database Acc Id Source(s)
COSMIC TRIM39-RPP21 COSMIC
Ensembl Genes ENSG00000239927 UniProtKB/TrEMBL
  ENSG00000241863 UniProtKB/TrEMBL
  ENSG00000248167 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENST00000552257.4 UniProtKB/TrEMBL
  ENST00000552950.4 UniProtKB/TrEMBL
  ENST00000623385 ENTREZGENE
  ENST00000623385.3 UniProtKB/TrEMBL
Gene3D-CATH 2.60.120.920 UniProtKB/TrEMBL
  3.30.40.10 UniProtKB/TrEMBL
  6.20.50.20 UniProtKB/TrEMBL
  Classic Zinc Finger UniProtKB/TrEMBL
GTEx ENSG00000239927 GTEx
  ENSG00000241863 GTEx
  ENSG00000248167 GTEx
HGNC ID HGNC:38845 ENTREZGENE
Human Proteome Map TRIM39-RPP21 Human Proteome Map
InterPro B30.2/SPRY UniProtKB/TrEMBL
  B30.2/SPRY_sf UniProtKB/TrEMBL
  Butyrophylin UniProtKB/TrEMBL
  ConA-like_dom UniProtKB/TrEMBL
  PRY UniProtKB/TrEMBL
  Rpr2 UniProtKB/TrEMBL
  Znf_B-box UniProtKB/TrEMBL
  Znf_RING UniProtKB/TrEMBL
  Znf_RING/FYVE/PHD UniProtKB/TrEMBL
  Znf_RING_CS UniProtKB/TrEMBL
KEGG Report hsa:202658 UniProtKB/TrEMBL
NCBI Gene 202658 ENTREZGENE
PANTHER E3 UBIQUITIN-PROTEIN LIGASE TRIM UniProtKB/TrEMBL
  E3 UBIQUITIN-PROTEIN LIGASE TRIM39 UniProtKB/TrEMBL
Pfam PRY UniProtKB/TrEMBL
  Rpr2 UniProtKB/TrEMBL
  zf-B_box UniProtKB/TrEMBL
  zf-C3HC4_4 UniProtKB/TrEMBL
PRINTS BUTYPHLNCDUF UniProtKB/TrEMBL
PROSITE B302_SPRY UniProtKB/TrEMBL
  ZF_BBOX UniProtKB/TrEMBL
  ZF_RING_1 UniProtKB/TrEMBL
  ZF_RING_2 UniProtKB/TrEMBL
SMART BBOX UniProtKB/TrEMBL
  PRY UniProtKB/TrEMBL
  RING UniProtKB/TrEMBL
Superfamily-SCOP B-box zinc-binding domain UniProtKB/TrEMBL
  ConA_like_lec_gl UniProtKB/TrEMBL
  RING/U-box UniProtKB/TrEMBL
UniProt A0A096LP39 ENTREZGENE, UniProtKB/TrEMBL
  A0A0G2JKY0 ENTREZGENE
  A0A140TA46 ENTREZGENE
  A6ZJ12_HUMAN UniProtKB/TrEMBL